diff --git a/test/functional/page_objects/common_page.ts b/test/functional/page_objects/common_page.ts
index 9e48ac1ea7e36..215d552d07f7d 100644
--- a/test/functional/page_objects/common_page.ts
+++ b/test/functional/page_objects/common_page.ts
@@ -411,9 +411,18 @@ export class CommonPageObject extends FtrService {
    * Clicks cancel button on modal
    * @param overlayWillStay pass in true if your test will show multiple modals in succession
    */
-  async clickCancelOnModal(overlayWillStay = true) {
+  async clickCancelOnModal(overlayWillStay = true, ignorePageLeaveWarning = false) {
     this.log.debug('Clicking modal cancel');
-    await this.testSubjects.click('confirmModalCancelButton');
+    await this.testSubjects.exists('confirmModalTitleText');
+
+    await this.retry.try(async () => {
+      const warning = await this.testSubjects.exists('confirmModalTitleText');
+      if (warning) {
+        await this.testSubjects.click(
+          ignorePageLeaveWarning ? 'confirmModalConfirmButton' : 'confirmModalCancelButton'
+        );
+      }
+    });
     if (!overlayWillStay) {
       await this.ensureModalOverlayHidden();
     }
diff --git a/test/functional/services/apps_menu.ts b/test/functional/services/apps_menu.ts
index 9fb8e36476f3e..0f63166477883 100644
--- a/test/functional/services/apps_menu.ts
+++ b/test/functional/services/apps_menu.ts
@@ -59,6 +59,7 @@ export class AppsMenuService extends FtrService {
     if (!(await this.testSubjects.exists('collapsibleNav'))) {
       await this.testSubjects.click('toggleNavButton');
     }
+    await this.testSubjects.exists('collapsibleNav');
   }
 
   /**
diff --git a/test/plugin_functional/plugins/core_plugin_appleave/public/plugin.tsx b/test/plugin_functional/plugins/core_plugin_appleave/public/plugin.tsx
index aab64fc657696..a5107a375d8a0 100644
--- a/test/plugin_functional/plugins/core_plugin_appleave/public/plugin.tsx
+++ b/test/plugin_functional/plugins/core_plugin_appleave/public/plugin.tsx
@@ -6,7 +6,7 @@
  * Side Public License, v 1.
  */
 
-import { Plugin, CoreSetup } from '@kbn/core/public';
+import { Plugin, CoreSetup, DEFAULT_APP_CATEGORIES } from '@kbn/core/public';
 
 export class CoreAppLeavePlugin
   implements Plugin<CoreAppLeavePluginSetup, CoreAppLeavePluginStart>
@@ -15,6 +15,8 @@ export class CoreAppLeavePlugin
     core.application.register({
       id: 'appleave1',
       title: 'AppLeave 1',
+      appRoute: '/app/appleave1',
+      category: DEFAULT_APP_CATEGORIES.kibana,
       async mount(params) {
         const { renderApp } = await import('./application');
         params.onAppLeave((actions) => actions.confirm('confirm-message', 'confirm-title'));
@@ -24,9 +26,11 @@ export class CoreAppLeavePlugin
     core.application.register({
       id: 'appleave2',
       title: 'AppLeave 2',
+      appRoute: '/app/appleave2',
+      category: DEFAULT_APP_CATEGORIES.kibana,
       async mount(params) {
         const { renderApp } = await import('./application');
-        params.onAppLeave((actions) => actions.default());
+        params.onAppLeave((actions) => actions.confirm('confirm-message', 'confirm-title'));
         return renderApp('AppLeave 2', params);
       },
     });
diff --git a/test/plugin_functional/plugins/core_plugin_deep_links/public/application.tsx b/test/plugin_functional/plugins/core_plugin_deep_links/public/application.tsx
index 345ffbd5b47d2..d816254dbf39b 100644
--- a/test/plugin_functional/plugins/core_plugin_deep_links/public/application.tsx
+++ b/test/plugin_functional/plugins/core_plugin_deep_links/public/application.tsx
@@ -50,7 +50,7 @@ const PageA = () => (
     <EuiPageHeader>
       <EuiPageHeaderSection>
         <EuiTitle size="l">
-          <h1>DL Page A</h1>
+          <h1>DL page A</h1>
         </EuiTitle>
       </EuiPageHeaderSection>
     </EuiPageHeader>
@@ -70,7 +70,7 @@ const PageB = () => (
     <EuiPageHeader>
       <EuiPageHeaderSection>
         <EuiTitle size="l">
-          <h1>DL Page B</h1>
+          <h1>DL page B</h1>
         </EuiTitle>
       </EuiPageHeaderSection>
     </EuiPageHeader>
diff --git a/test/plugin_functional/plugins/core_plugin_deep_links/public/plugin.tsx b/test/plugin_functional/plugins/core_plugin_deep_links/public/plugin.tsx
index f7e3102f0b230..2c1af49e7eb6b 100644
--- a/test/plugin_functional/plugins/core_plugin_deep_links/public/plugin.tsx
+++ b/test/plugin_functional/plugins/core_plugin_deep_links/public/plugin.tsx
@@ -29,7 +29,7 @@ export class CorePluginDeepLinksPlugin
         },
         {
           id: 'pageA',
-          title: 'DL Page A',
+          title: 'DL page A',
           path: '/page-a',
           navLinkStatus: AppNavLinkStatus.visible,
         },
@@ -39,7 +39,7 @@ export class CorePluginDeepLinksPlugin
           deepLinks: [
             {
               id: 'pageB',
-              title: 'DL Page B',
+              title: 'DL page B',
               path: '/page-b',
               navLinkStatus: AppNavLinkStatus.visible,
             },
@@ -47,7 +47,7 @@ export class CorePluginDeepLinksPlugin
         },
         {
           id: 'pageC',
-          title: 'DL Page C',
+          title: 'DL page C',
           path: '/page-c',
           // navLinkStatus hidden by default
         },
diff --git a/test/plugin_functional/test_suites/core_plugins/application_deep_links.ts b/test/plugin_functional/test_suites/core_plugins/application_deep_links.ts
index 8d558dafa68f5..98a824c007a62 100644
--- a/test/plugin_functional/test_suites/core_plugins/application_deep_links.ts
+++ b/test/plugin_functional/test_suites/core_plugins/application_deep_links.ts
@@ -18,6 +18,7 @@ export default function ({ getService, getPageObjects }: PluginFunctionalProvide
   const testSubjects = getService('testSubjects');
   const retry = getService('retry');
   const esArchiver = getService('esArchiver');
+  const log = getService('log');
 
   const loadingScreenNotShown = async () =>
     expect(await testSubjects.exists('kbnLoadingMessage')).to.be(false);
@@ -35,12 +36,20 @@ export default function ({ getService, getPageObjects }: PluginFunctionalProvide
   const waitForUrlToBe = (pathname?: string, search?: string) => {
     const expectedUrl = getKibanaUrl(pathname, search);
     return retry.waitFor(`Url to be ${expectedUrl}`, async () => {
-      return (await browser.getCurrentUrl()) === expectedUrl;
+      const currentUrl = await browser.getCurrentUrl();
+      log?.debug(`waiting for currentUrl ${currentUrl} to be expectedUrl ${expectedUrl}`);
+      return currentUrl === expectedUrl;
     });
   };
 
-  // Failing: See https://github.com/elastic/kibana/issues/166893
-  describe.skip('application deep links navigation', function describeDeepLinksTests() {
+  const navigateToAppLinks = async (subject: string) => {
+    if (!(await testSubjects.exists(subject))) {
+      log.debug(`side nav in app not in DOM`);
+    }
+    await testSubjects.click(subject);
+  };
+
+  describe('application deep links navigation', function describeDeepLinksTests() {
     before(async () => {
       await esArchiver.emptyKibanaIndex();
       await PageObjects.common.navigateToApp('dl');
@@ -51,28 +60,29 @@ export default function ({ getService, getPageObjects }: PluginFunctionalProvide
     });
 
     it('should navigate to page A when navlink is clicked', async () => {
-      await appsMenu.clickLink('DL Page A');
+      await navigateToAppLinks('dlNavPageA');
       await waitForUrlToBe('/app/dl/page-a');
       await loadingScreenNotShown();
-      await testSubjects.existOrFail('dlAppPageA');
+      await testSubjects.existOrFail('dlNavPageA');
     });
 
     it('should be able to use the back button to navigate back to previous deep link', async () => {
       await browser.goBack();
       await waitForUrlToBe('/app/dl/home');
       await loadingScreenNotShown();
-      await testSubjects.existOrFail('dlAppHome');
+      await testSubjects.existOrFail('dlNavHome');
     });
 
     it('should navigate to nested page B when navlink is clicked', async () => {
-      await appsMenu.clickLink('DL Page B');
+      await navigateToAppLinks('dlNavDeepPageB');
       await waitForUrlToBe('/app/dl/page-b');
       await loadingScreenNotShown();
-      await testSubjects.existOrFail('dlAppPageB');
+      await testSubjects.existOrFail('dlNavDeepPageB');
     });
 
     it('should navigate to Home when navlink is clicked inside the defined category group', async () => {
       await appsMenu.clickLink('DL Home', { category: 'securitySolution' });
+      await navigateToAppLinks('dlAppHome');
       await waitForUrlToBe('/app/dl/home');
       await loadingScreenNotShown();
       await testSubjects.existOrFail('dlAppHome');
@@ -82,14 +92,14 @@ export default function ({ getService, getPageObjects }: PluginFunctionalProvide
       await testSubjects.click('dlNavDeepPageB');
       await waitForUrlToBe('/app/dl/page-b');
       await loadingScreenNotShown();
-      await testSubjects.existOrFail('dlAppPageB');
+      await testSubjects.existOrFail('dlNavDeepPageB');
     });
 
     it('should navigate to nested page A using navigateToApp deepLinkId', async () => {
       await testSubjects.click('dlNavDeepPageAById');
       await waitForUrlToBe('/app/dl/page-a');
       await loadingScreenNotShown();
-      await testSubjects.existOrFail('dlAppPageA');
+      await testSubjects.existOrFail('dlNavPageA');
     });
 
     it('should not display hidden deep links', async () => {
diff --git a/test/plugin_functional/test_suites/core_plugins/application_leave_confirm.ts b/test/plugin_functional/test_suites/core_plugins/application_leave_confirm.ts
index 987796be3a6a7..4d0f837108b73 100644
--- a/test/plugin_functional/test_suites/core_plugins/application_leave_confirm.ts
+++ b/test/plugin_functional/test_suites/core_plugins/application_leave_confirm.ts
@@ -6,8 +6,8 @@
  * Side Public License, v 1.
  */
 
-import url from 'url';
 import expect from '@kbn/expect';
+import url from 'url';
 import { PluginFunctionalProviderContext } from '../../services';
 
 const getKibanaUrl = (pathname?: string, search?: string) =>
@@ -20,30 +20,96 @@ const getKibanaUrl = (pathname?: string, search?: string) =>
   });
 
 export default function ({ getService, getPageObjects }: PluginFunctionalProviderContext) {
-  const PageObjects = getPageObjects(['common']);
+  const PageObjects = getPageObjects(['common', 'header']);
   const browser = getService('browser');
   const appsMenu = getService('appsMenu');
+  const log = getService('log');
+  const retry = getService('retry');
   const testSubjects = getService('testSubjects');
+  const config = getService('config');
+
+  const waitForUrlToBe = async (pathname?: string, search?: string) => {
+    const expectedUrl = getKibanaUrl(pathname, search);
+    return await retry.waitFor(`Url to be ${expectedUrl}`, async () => {
+      const currentUrl = await browser.getCurrentUrl();
+      log.debug(`waiting for currentUrl ${currentUrl} to be expectedUrl ${expectedUrl}`);
+      return currentUrl === expectedUrl;
+    });
+  };
+
+  const ensureModalOpen = async (
+    defaultTryTimeout: number,
+    attempts: number,
+    timeMultiplier: number,
+    action: 'cancel' | 'confirm',
+    linkText: string = 'home'
+  ): Promise<void> => {
+    let isConfirmCancelModalOpenState = false;
 
-  // Failing: See https://github.com/elastic/kibana/issues/75963
-  // Failing: See https://github.com/elastic/kibana/issues/166838
-  describe.skip('application using leave confirmation', () => {
+    await retry.tryForTime(defaultTryTimeout * timeMultiplier, async () => {
+      await appsMenu.clickLink(linkText);
+      isConfirmCancelModalOpenState = await testSubjects.exists('confirmModalTitleText', {
+        allowHidden: true,
+        timeout: defaultTryTimeout * timeMultiplier,
+      });
+    });
+    if (isConfirmCancelModalOpenState) {
+      log.debug(`defaultTryTimeout * ${timeMultiplier} is long enough`);
+      return action === 'cancel'
+        ? await PageObjects.common.clickCancelOnModal(true, false)
+        : await PageObjects.common.clickConfirmOnModal();
+    } else {
+      log.debug(`defaultTryTimeout * ${timeMultiplier} is not long enough`);
+      return await ensureModalOpen(
+        defaultTryTimeout,
+        (attempts = attempts > 0 ? attempts - 1 : 0),
+        (timeMultiplier = timeMultiplier < 10 ? timeMultiplier + 1 : 10),
+        action,
+        linkText
+      );
+    }
+  };
+
+  describe('application using leave confirmation', () => {
+    const defaultTryTimeout = config.get('timeouts.try');
+    const attempts = 5;
     describe('when navigating to another app', () => {
+      const timeMultiplier = 10;
+      beforeEach(async () => {
+        await PageObjects.common.navigateToApp('home');
+      });
       it('prevents navigation if user click cancel on the confirmation dialog', async () => {
         await PageObjects.common.navigateToApp('appleave1');
-        await appsMenu.clickLink('AppLeave 2');
+        await PageObjects.header.waitUntilLoadingHasFinished();
+        await waitForUrlToBe('/app/appleave1');
 
-        await testSubjects.existOrFail('appLeaveConfirmModal');
-        await PageObjects.common.clickCancelOnModal(false);
-        expect(await browser.getCurrentUrl()).to.eql(getKibanaUrl('/app/appleave1'));
+        await ensureModalOpen(defaultTryTimeout, attempts, timeMultiplier, 'cancel', 'AppLeave 2');
+        await PageObjects.header.waitUntilLoadingHasFinished();
+        await retry.waitFor('navigate to appleave1', async () => {
+          const currentUrl = await browser.getCurrentUrl();
+          log.debug(`currentUrl ${currentUrl}`);
+          return currentUrl.includes('appleave1');
+        });
+        const currentUrl = await browser.getCurrentUrl();
+        expect(currentUrl).to.contain('appleave1');
+        await PageObjects.common.navigateToApp('home');
       });
+
       it('allows navigation if user click confirm on the confirmation dialog', async () => {
         await PageObjects.common.navigateToApp('appleave1');
-        await appsMenu.clickLink('AppLeave 2');
+        await PageObjects.header.waitUntilLoadingHasFinished();
+        await waitForUrlToBe('/app/appleave1');
 
-        await testSubjects.existOrFail('appLeaveConfirmModal');
-        await PageObjects.common.clickConfirmOnModal();
-        expect(await browser.getCurrentUrl()).to.eql(getKibanaUrl('/app/appleave2'));
+        await ensureModalOpen(defaultTryTimeout, attempts, timeMultiplier, 'confirm', 'AppLeave 2');
+        await PageObjects.header.waitUntilLoadingHasFinished();
+        await retry.waitFor('navigate to appleave1', async () => {
+          const currentUrl = await browser.getCurrentUrl();
+          log.debug(`currentUrl ${currentUrl}`);
+          return currentUrl.includes('appleave2');
+        });
+        const currentUrl = await browser.getCurrentUrl();
+        expect(currentUrl).to.contain('appleave2');
+        await PageObjects.common.navigateToApp('home');
       });
     });
   });